The commuter rail agency’s new CEO, Alex Clifford, said Friday that rising diesel fuel prices and the state of Illinois’ continuing inability to pay subsidies in a timely fashion may leave Metra with a $100 million 2011 budget shortfall.

Clifford has said for several months that if fuel prices remained at the levels at which Metra had budgeted — $2.35 a gallon – the rail agency would have a surplus.

Instead, prices were $2.62 a gallon in early January and have escalated to roughly $3.15 a gallon. Although prices have leveled off in the past month, Clifford said the damage is already done.

Metra’s board members will meet in special session June 23 to take a closer look at the budget — and their options.

No game plan is expected to be ready that day, though, said a Metra spokesperson.

In the past, Metra officials have said that a 5 percent fare increase would only generate about $10 million for the agency.

Metra expects to gain several million dollars this fall, when free rides for senior citizens are limited to those low-income seniors who are registered in the state’s Circuit Breaker program.

At the Metra board’s meeting Friday, Clifford highlighted a graphic that shows how Metra’s fares have increased in comparison with the average increases at other big-city transit agencies. The graphic shows that Metra has lagged well behind for years and that the gap continues to grow.

Metra has shifted money earmarked for capital projects to pay operating bills in all but two of the last eight years. Clifford said the practice siphons off money Metra needs badly as repair and reconstruction needs multiply.